From 3340f1ded16bdf47f1a19bd088e31163c37b073f Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Fri, 14 Feb 2020 11:05:56 +0100
Subject: [PATCH] add nextflow scripts for ribotish
---
src/nf_modules/ribotish/ribotish.config | 42 ++++++++++++++++++
src/nf_modules/ribotish/ribotish_predict.nf | 49 +++++++++++++++++++++
src/nf_modules/ribotish/ribotish_quality.nf | 41 +++++++++++++++++
src/nf_modules/ribotish/tests.sh | 6 +++
4 files changed, 138 insertions(+)
create mode 100644 src/nf_modules/ribotish/ribotish.config
create mode 100644 src/nf_modules/ribotish/ribotish_predict.nf
create mode 100644 src/nf_modules/ribotish/ribotish_quality.nf
create mode 100755 src/nf_modules/ribotish/tests.sh
diff --git a/src/nf_modules/ribotish/ribotish.config b/src/nf_modules/ribotish/ribotish.config
new file mode 100644
index 00000000..aa1d2951
--- /dev/null
+++ b/src/nf_modules/ribotish/ribotish.config
@@ -0,0 +1,42 @@
+profiles {
+ docker {
+ docker.temp = 'auto'
+ docker.enabled = true
+ process {
+ withName: ribotish_quality {
+ container = "lbmc/ribotish:0.2.4"
+ cpus = 4
+ }
+ withName: ribotish_pred {
+ container = "lbmc/ribotish:0.2.4"
+ cpus = 4
+ }
+ }
+ }
+ psmn{
+ process{
+ withName: ribotish_quality {
+ beforeScript = "source .conda_psmn.sh"
+ conda = "src/.conda_envs/ribotish_0.2.4"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 8
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ withName: ribotish_pred {
+ beforeScript = "source .conda_psmn.sh"
+ conda = "src/.conda_envs/ribotish_0.2.4"
+ executor = "sge"
+ clusterOptions = "-cwd -V"
+ cpus = 8
+ memory = "30GB"
+ time = "24h"
+ queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+ penv = 'openmp16'
+ }
+ }
+ }
+}
diff --git a/src/nf_modules/ribotish/ribotish_predict.nf b/src/nf_modules/ribotish/ribotish_predict.nf
new file mode 100644
index 00000000..a07b16eb
--- /dev/null
+++ b/src/nf_modules/ribotish/ribotish_predict.nf
@@ -0,0 +1,49 @@
+params.bam = "data/*{Harr,CHX}*.bam"
+params.bai = "data/*{Harr,CHX}*.bam.bai"
+params.gff = "data/*.gtf"
+params.genome = "data/*.fa"
+params.quality = "results/quality/*"
+
+log.info "bam files : ${params.bam}"
+
+Channel
+.fromFilePairs( params.bam )
+.ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+.set { bam_files }
+Channel
+.fromFilePairs( params.bai )
+.ifEmpty { error "Cannot find any bai files matching: ${params.bai}" }
+.set { bai_files }
+Channel
+ .fromPath( params.gff )
+ .ifEmpty { error "Cannot find any gff files matching: ${params.gff}" }
+ .set { gff_files }
+Channel
+ .fromPath( params.genome )
+ .ifEmpty { error "Cannot find any fasta files matching: ${params.genome}" }
+ .set { genome_files }
+Channel
+ .fromPath( params.files )
+ .ifEmpty { error "Cannot find any files matching: ${params.quality}" }
+ .set { quality_files }
+
+process ribotish_pred {
+ tag "$file_id"
+ publishDir "results/pred/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from bam_files
+ set bai_id, file(bai) from bai_files
+ file gff from gff_files.collect()
+ file genome from genome_files.collect()
+ file quality from quality_files.collect()
+
+ output:
+ set file_id, "*" into pred
+
+ script:
+"""
+ribotish predict -t ${bam[0]} -b ${bam[1]} -g ${gff} -f ${genome} \
+-o ${file_id}_pred.txt --harr -p ${task.cpus} --alt
+"""
+}
diff --git a/src/nf_modules/ribotish/ribotish_quality.nf b/src/nf_modules/ribotish/ribotish_quality.nf
new file mode 100644
index 00000000..2f5bcd6a
--- /dev/null
+++ b/src/nf_modules/ribotish/ribotish_quality.nf
@@ -0,0 +1,41 @@
+params.bam = "data/*{.bam,.bam.bai}"
+params.gff = "data/*.gtf"
+params.length = "25,35"
+params.th = "0.5"
+
+log.info "bam files : ${params.bam}"
+
+Channel
+ .fromFilePairs( params.bam )
+ .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+ .set { bam_files }
+Channel
+ .fromPath( params.gff )
+ .ifEmpty { error "Cannot find any gff files matching: ${params.gff}" }
+ .set { gff_files }
+
+process ribotish_quality {
+ tag "$file_id"
+ publishDir "results/quality/", mode: 'copy'
+
+ input:
+ set file_id, file(bam) from bam_files
+ file gff from gff_files.collect()
+
+ output:
+ set file_id, "*" into quality
+
+ script:
+ tis_parameters = ""
+ if (bam =~ /Harr/) {
+ tis_parameters = "-t"
+ }
+"""
+ribotish quality -b ${bam[0]} \
+ -g ${gff} \
+ -p ${task.cpus} \
+ -l ${params.length} \
+ --th ${params.th} \
+ ${tis_parameters}
+"""
+}
diff --git a/src/nf_modules/ribotish/tests.sh b/src/nf_modules/ribotish/tests.sh
new file mode 100755
index 00000000..0894f2bc
--- /dev/null
+++ b/src/nf_modules/ribotish/tests.sh
@@ -0,0 +1,6 @@
+./nextflow src/nf_modules/ribotish/ribotish_quality.nf \
+ -c src/nf_modules/ribotish/ribotish.config \
+ -profile docker \
+ --bam "data/tiny_dataset/map/tiny_v2.bam" \
+ --gff "data/tiny_dataset/annot/tiny.gtf" \
+ -resume
--
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